The Pajarito Plateau in northern New Mexico, on which the Los Alamos National Laboratory (LANL) is situated, is characterized by a deep vadose zone overlying the regional aquifer of the Espanola Basin. In this study, conceptual models of vadose-zone flow and transport processes are developed through the interpretation of field data and synthesis with numerical models. The types of data incorporated into the development of the conceptual model include moisture content and pore-water chemical compositions in borehole samples, a fluid injection experiment with monitoring of moisture plume migration, contaminant concentration distributions, air permeability testing, and downhole air pressure responses to barometric signals. The observations include sites under natural conditions and sites experiencing periods of enhanced water application due to surface disturbances resulting from LANL facilities. The key conceptual model elements describe percolation of water through both fractured and relatively unfractured volcanic tuffs, buried sedimentary formations and basalts. The conceptual model differentiates the rate of these processes by their location and surface hydrologic setting, including wet and dry canyons, natural mesas and disturbed mesas. Infiltration beneath wet canyons is the highest with rates on the order of meters per year (100 - 1000 mm/yr). Transport to the regional aquifer beneath wet canyons is on the order of decades to hundreds of years, depending on the thicknesses of the various hydrostratigraphic layers. Perched water is typically found beneath wetter canyons, resulting from low-permeability units such as unfractured regions of the basalt flows and buried soils. Percolation through the volcanic tuffs is generally considered to be via matrix-dominated flow, whereas fracture flow may play a key role in contaminant transport through basalt units beneath wet canyons. Infiltration beneath dry canyons and dry mesas is much slower (ten mm/yr or less), yielding transport times to the aquifer of hundreds to several thousands of years. However, long-term surface disturbances at mesa-top locations may alter infiltration rates such that at a local scale, they approach those of wetter canyons.